Here are links to software that we are developing, for code developed at NYU or ISB the code is freely available, for codes developed as part of larger multi-institution efforts we provide links to those efforts. In general we are an open source shop.

Software:

cMonkey: Learns significant clusters, control elements and subnetworks from diverse systems-biology data. Written in R, free after publication. [download]

Inferelator: Learns parsimonious regulatory networks from systems biology datasets. Companion to cMonkey. Written in R, free after publication. [download]

Rosetta: a state of the art structure prediction and way more (licenced via University of Washington)

Robetta: web server for rosetta structure prediction and Ginzu protein-domain parsing (submit a few of your favorite unknown proteins here).

BioNetBuilder: BioNetBuilder is a Cytoscape plugIn that offers a user friendly interface to create biological networks integrated from several databases. [webstart]

Cytoscape: A systems biology data-integration and viz platform. Initially developed to map expression data onto biological networks.

The Gaggle: Data-integration platform (developed by Paul Shannon). A way to manage many different data-types and views as a mutli-threaded gaggle controlled by the gaggle-boss.

Databases:

Yeast-Resource center fold/fnx database: Rosetta and Ginzu predictions for Yeast genomes, and a whole lot more. This was done in collaboration with Trisha Davis, David Baker, Lars Malmstroem, Mike Riffle (all at UW). [available soon]

Human Proteome Folding Results: Rosetta and Ginzu predictions for over 90 complete genomes, and a whole lot more. Fold and function predictions generated on the WCGrid. This was done in collaboration with Trisha Davis, David Baker, Lars Malmstroem, Mike Riffle (all at UW). [availiable soon]